title: Antibody-specified B-cell epitope prediction in line with the principle of context-awareness.
abstract: Context-awareness is a characteristic in the recognition between antigens and antibodies, highlighting the reconfiguration of epitope residues when an antigen interacts with a different antibody. A coarse binary classification of antigen regions into epitopes, or nonepitopes without specifying antibodies may not accurately reflect this biological reality. Therefore, we study an antibody-specified epitope prediction problem in line with this principle. This problem is new and challenging as we pinpoint a subset of the antigenic residues from an antigen when it binds to a specific antibody. We introduce two kinds of associations of the contextual awareness: 1) residues-residues pairing preference, and 2) the dependence between sets of contact residue pairs. Preference plays a bridging role to link interacting paratope and epitope residues while dependence is used to extend the association from one-dimension to two-dimension. The paratope/epitope residues' relative composition, cooperativity ratios, and Markov properties are also utilized to enhance our method. A nonredundant data set containing 80 antibody-antigen complexes is compiled and used in the evaluation. The results show that our method yields a good performance on antibody-specified epitope prediction. On the traditional antibody-ignored epitope prediction problem, a simplified version of our method can produce a competitive, sometimes much better, performance in comparison with three structure-based predictors.
authors.affiliation: School of Computer Engineering, Bioinformatics Research Center, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798. S080011@e.ntu.edu.sg
authors.forename: Liang
authors.initials: L
authors.lastname: Zhao
authors.forename: Limsoon
authors.initials: L
authors.lastname: Wong
authors.forename: Jinyan
authors.initials: J
authors.lastname: Li
mesh_terms: D000906:Antibodies / Q000737:chemistry*; D000936:Antigen-Antibody Complex / Q000737:chemistry; D001665:Binding Sites; D001666:Binding Sites, Antibody; D030562:Databases, Protein; D018604:Epitope Mapping; D018985:Epitopes, B-Lymphocyte / Q000737:chemistry*; D008390:Markov Chains; D008958:Models, Molecular; D011487:Protein Conformation
chemical_list: D000906:Antibodies; D000936:Antigen-Antibody Complex; D018985:Epitopes, B-Lymphocyte